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https://www.readbyqxmd.com/read/28406496/strategic-and-practical-guidelines-for-successful-structured-illumination-microscopy
#1
Justin Demmerle, Cassandravictoria Innocent, Alison J North, Graeme Ball, Marcel Müller, Ezequiel Miron, Atsushi Matsuda, Ian M Dobbie, Yolanda Markaki, Lothar Schermelleh
Linear 2D- or 3D-structured illumination microscopy (SIM or3D-SIM, respectively) enables multicolor volumetric imaging of fixed and live specimens with subdiffraction resolution in all spatial dimensions. However, the reliance of SIM on algorithmic post-processing renders it particularly sensitive to artifacts that may reduce resolution, compromise data and its interpretations, and drain resources in terms of money and time spent. Here we present a protocol that allows users to generate high-quality SIM data while accounting and correcting for common artifacts...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28406495/quantitative-3d-structured-illumination-microscopy-of-nuclear-structures
#2
Felix Kraus, Ezequiel Miron, Justin Demmerle, Tsotne Chitiashvili, Alexei Budco, Quentin Alle, Atsushi Matsuda, Heinrich Leonhardt, Lothar Schermelleh, Yolanda Markaki
3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28364021/lateral-segregation-of-photosystem-i-in-cyanobacterial-thylakoids
#3
Craig MacGregor-Chatwin, Melih Sener, Samuel F H Barnett, Andrew Hitchcock, Meghan C Barnhart-Dailey, Karim Maghlaoui, James Barber, Jerilyn A Timlin, Klaus Schulten, Christopher Neil Hunter
Photosystem I (PSI) is the dominant photosystem in cyanobacteria and it plays a pivotal role in cyanobacterial metabolism. Despite its biological importance, the native organisation of PSI in cyanobacterial thylakoid membranes is poorly understood. Here, we use atomic force microscopy (AFM) to show that ordered, extensive macromolecular arrays of PSI complexes are present in thylakoids from Thermosynechococcus (T.) elongatus, Synechococcus sp. PCC 7002 and Synechocystis sp PCC 6803. Hyperspectral confocal fluorescence microscopy (HCFM) and three-dimensional structured illumination microscopy (3D-SIM) of Synechocystis sp PCC 6803 cells visualise PSI domains within the context of the complete thylakoid system...
March 31, 2017: Plant Cell
https://www.readbyqxmd.com/read/28332827/subcellular-chemical-imaging-of-antibiotics-in-single-bacteria-using-c60-secondary-ion-mass-spectrometry
#4
Hua Tian, David A Six, Thomas Krucker, Jennifer A Leeds, Nicholas Winograd
The inherent difficulty of discovering new and effective antibacterials and the rapid development of resistance particularly in Gram-negative bacteria, illustrates the urgent need for new methods that enable rational drug design. Here we report the development of 3D imaging cluster secondary ion mass spectrometry (SIMS) as a label-free approach to chemically map small molecules in aggregated and single Escherichia coli cells, with ~300 nm spatial resolution and high chemical sensitivity. The feasibility of quantitative analysis was explored, and a non-linear relationship between treatment dose and signal for tetracycline and ampicillin, two clinically-used antibacterials, was observed...
March 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28326349/quantitative-in-vivo-micro-computed-tomography-for-assessment-of-age-dependent-changes-in-murine-whole-body-composition
#5
Kim L Beaucage, Steven I Pollmann, Stephen M Sims, S Jeffrey Dixon, David W Holdsworth
Micro-computed tomography (micro-CT) is used routinely to quantify skeletal tissue mass in small animal models. Our goal was to evaluate repeated in vivo micro-CT imaging for monitoring whole-body composition in studies of growth and aging in mice. Male mice from 2 to 52 weeks of age were anesthetized and imaged using an eXplore Locus Ultra and/or eXplore speCZT scanner. Images were reconstructed into 3D volumes, signal-intensity thresholds were used to classify each voxel as adipose, lean or skeletal tissue, and tissue masses were calculated from known density values...
December 2016: Bone Reports
https://www.readbyqxmd.com/read/28323041/quantitative-analyses-of-the-3d-nuclear-landscape-recorded-with-super-resolved-fluorescence-microscopy
#6
Volker J Schmid, Marion Cremer, Thomas Cremer
Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction...
March 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28252396/joint-reconstruction-strategy-for-structured-illumination-microscopy-with-unknown-illuminations
#7
Simon Labouesse, Awoke Negash, Jerome Idier, Sebastien Bourguignon, Thomas Mangeat, Penghuan Liu, Anne Sentenac, Marc Allain
The blind structured illumination microscopy strategy proposed by Mudry et al. is fully re-founded in this paper, unveiling the central role of the sparsity of the illumination patterns in the mechanism that drives super-resolution in the method. A numerical analysis shows that the resolving power of the method can be further enhanced with optimized one-photon or two-photon speckle illuminations. A much improved numerical implementation is provided for the reconstruction problem under the image positivity constraint...
May 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28248385/effect-of-oil-on-an-electrowetting-lenticular-lens-and-related-optical-characteristics
#8
Dooseub Shin, Junoh Kim, Cheoljoong Kim, Gyo Hyun Koo, Jee Hoon Sim, Junsik Lee, Yong Hyub Won
While there are many ways to realize autostereoscopic 2D/3D switchable displays, the electrowetting lenticular lens is superior due to the high optical efficiency and short response time. In this paper, we propose a more stable electrowetting lenticular lens by controlling the quantity of oil. With a large amount of oil, the oil layer was broken and the lenticular lens was damaged at relatively low voltage. Therefore, controlling the amount of oil is crucial to obtain the required dioptric power with stability...
March 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/28240420/clinical-utility-of-multipolar-ablation-with-a-three-dimensional-simulator-system-for-patients-with-liver-cancer
#9
Masashi Hirooka, Yohei Koizumi, Yusuke Imai, Yoshiko Nakamura, Atsushi Yukimoto, Takao Watanabe, Osamu Yoshida, Yoshio Tokumoto, Masanori Abe, Yoichi Hiasa
BACKGROUND AND AIM: To confirm the efficacy of multipolar ablation with a new simulator system, 3D sim-Navigator, for patients with hepatocellular carcinoma by assessing relapse-free survival and shape of the ablation volume under clinical conditions. METHODS: All participants provided written, informed consent, and study protocols were approved by the institutional ethics committee. Twenty-seven patients with 27 nodules were treated by no-touch ablation using the new simulator system...
February 27, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28192239/super-silac-mix-coupled-with-sim-aims-assays-for-targeted-verification-of-phosphopeptides-discovered-in-a-large-scale-phosphoproteome-analysis-of-hepatocellular-carcinoma
#10
Yu-Tsun Lin, Kun-Yi Chien, Chia-Chun Wu, Wen-Yu Chang, Lichieh Julie Chu, Min-Chi Chen, Chau-Ting Yeh, Jau-Song Yu
Plentiful studies have established a close association between aberrant phosphorylation and hepatocellular carcinoma (HCC). Here, we applied a quantitative phosphoproteomics platform combining dimethylation labeling and online 3D strong cation exchange chromatography (SCX)-titanium oxide (TiO2)/RP-LTQ-Orbitrap to compare phosphoproteomes between three pairs of HCC tissues and non-tumor counterparts. This analysis yielded 7868 quantifiable phosphopeptides and numerous up- or down-regulated candidates. Increased phosphorylation of LMNA and NIPA was confirmed using specific antibodies...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28155594/pbpk-modeling-a-predictive-eco-friendly-bio-waiver-tool-for-drug-research
#11
Baishakhi De, Koushik Bhandari, Ranjan Mukherjee, Prakash Katakam, Shanta K Adiki, Rohit Gundamaraju, Analava Mitra
BACKGROUND: The world has witnessed growing complexities in disease scenario influenced by the drastic changes in host-pathogen- environment triadic relation. Pharmaceutical R&Ds are in constant search of novel therapeutic entities to hasten transition of drug molecules from lab bench to patient bedside. Extensive animal studies and human pharmacokinetics are still the "gold standard" in investigational new drug research and bio-equivalency studies. Apart from cost, time and ethical issues on animal experimentation, burning questions arise relating to ecological disturbances, environmental hazards and biodiversity issues...
February 1, 2017: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/28103025/identification-of-the-first-selective-activin-receptor-like-kinase-1-inhibitor-a-reversible-version-of-l-783277
#12
Hanna Cho, Sandip Sengupta, Sean S H Jeon, Wooyoung Hur, Hwan Geun Choi, Hong-Seog Seo, Byung Joo Lee, Jeong Hun Kim, Minhwan Chung, Noo Li Jeon, Nam Doo Kim, Taebo Sim
We synthesized 1 (San78-130), a reversible version of L-783277, as a selective and potent ALK1 inhibitor. Our study showed that 1 possesses great kinase selectivity against a panel of 342 kinases and more potent activity against ALK1 than L-783277. Among the six ALK isotypes (ALK1-6), ALK1 is most significantly inhibited by compound 1. Compound 1 suppresses the BMP9-induced Smad1/5 pathway by mainly inhibiting ALK1 in C2C12 cells. Our molecular dynamics simulations suggest that H-bonding interaction between the C-4' hydroxyl group of 1 and Arg334 of ALK1 substantially contributes to the ALK1 inhibition...
February 6, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28100664/rab1-interacts-with-golph3-and-controls-golgi-structure-and-contractile-ring-constriction-during-cytokinesis-in-drosophila-melanogaster
#13
Stefano Sechi, Anna Frappaolo, Roberta Fraschini, Luisa Capalbo, Marco Gottardo, Giorgio Belloni, David M Glover, Alan Wainman, Maria Grazia Giansanti
Cytokinesis requires a tight coordination between actomyosin ring constriction and new membrane addition along the ingressing cleavage furrow. However, the molecular mechanisms underlying vesicle trafficking to the equatorial site and how this process is coupled with the dynamics of the contractile apparatus are poorly defined. Here we provide evidence for the requirement of Rab1 during cleavage furrow ingression in cytokinesis. We demonstrate that the gene omelette (omt) encodes the Drosophila orthologue of human Rab1 and is required for successful cytokinesis in both mitotic and meiotic dividing cells of Drosophila melanogaster We show that Rab1 protein colocalizes with the conserved oligomeric Golgi (COG) complex Cog7 subunit and the phosphatidylinositol 4-phosphate effector GOLPH3 at the Golgi stacks...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28072516/cobalt-based-single-ion-magnets-on-an-apatite-lattice-toward-patterned-arrays-for-magnetic-memories
#14
Pavel E Kazin, Mikhail A Zykin, Walter Schnelle, Yan V Zubavichus, Konstantin A Babeshkin, Victor A Tafeenko, Claudia Felser, Martin Jansen
Single-ion magnets (SIMs) that can maintain magnetization direction on an individual transition metal atom represent the smallest atomic-scale units for future magnetic data storage devices and molecular electronics. Here we present a robust extended inorganic solid hosting efficient SIM centers, as an alternative to molecular SIM crystals. We show that unique dioxocobaltate(II) ions, confined in the channels of strontium hydroxyapatite, exhibit classical SIM features with a large energy barrier for magnetization reversal (Ueff) of 51-59 cm(-1)...
January 10, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28068317/cryogenic-optical-localization-provides-3d-protein-structure-data-with-angstrom-resolution
#15
Siegfried Weisenburger, Daniel Boening, Benjamin Schomburg, Karin Giller, Stefan Becker, Christian Griesinger, Vahid Sandoghdar
We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology...
February 2017: Nature Methods
https://www.readbyqxmd.com/read/28059382/improving-the-performance-of-an-electrowetting-lenticular-lens-array-by-using-a-thin-polycarbonate-chamber
#16
Junsik Lee, Junoh Kim, Cheoljoong Kim, Dooseub Shin, Gyohyun Koo, Jee Hoon Sim, Yong Hyub Won
In this paper, we used a thin polycarbonate (PC) chamber to improve the performance of an electrowetting lenticular lens array. The polycarbonate chamber changed the radius of curvature (ROC) of the oil acting as a lens, which increased the dioptric power of the liquid lens to 1666.7D. The increase in dioptric power required a reduction in the distance between the optical center of the lens and the display pixels under the chamber, which was accomplished by reducing the thickness of the chamber. The optimal thickness of the chamber was determined to be 0...
December 26, 2016: Optics Express
https://www.readbyqxmd.com/read/28057763/the-ultrastructural-organization-of-actin-and-myosin-ii-filaments-in-the-contractile-ring-new-support-for-an-old-model-of-cytokinesis
#17
John H Henson, Casey E Ditzler, Aphnie Germain, Patrick M Irwin, Eric T Vogt, Shucheng Yang, Xufeng Wu, Charles B Shuster
Despite recent advances in our understanding of the components and spatial regulation of the contractile ring (CR), the precise ultrastructure of actin and myosin II within the animal cell CR remains an unanswered question. We used superresolution light microscopy and platinum replica transmission electron microscopy (TEM) to determine the structural organization of actin and myosin II in isolated cortical cytoskeletons prepared from dividing sea urchin embryos. Three-dimensional structured illumination microscopy indicated that within the CR, actin and myosin II filaments were organized into tightly packed linear arrays oriented along the axis of constriction and restricted to a narrow zone within the furrow...
March 1, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28047328/mo-fg-campus-jep3-05-evaluation-of-4d-ct-on-rails-target-localization-methods-for-free-breathing-liver-stereotactic-body-radiotherapy-sbrt
#18
J Fan, T Lin, L Jin, L Chen, I Veltchev, L Wang, A Eldib, O Chibani, B Wang, Q Xu, R Price, C Ma
PURPOSE: Liver SBRT patients unable to tolerate breath-hold for radiotherapy are treated free-breathing with image guidance. Target localization using 3D CBCT requires extra margins to accommodate the respiratory motion. The purpose of this study is to evaluate the accuracy and reproducibility of 4D CT-on-rails in target localization for free-breathing liver SBRT. METHODS: A Siemens SOMATOM CT-on-Rails 4D with Anzai Pressure Belt system was used both as the simulation and the localization CT...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/27996096/super-resolution-structure-of-dna-significantly-differs-in-buccal-cells-of-controls-and-alzheimer-s-patients
#19
Angeles Garcia, David Huang, Amanda Righolt, Christiaan Righolt, Maria Carmela Kalaw, Shubha Mathur, Elizabeth McAvoy, James Anderson, Angela Luedke, Justine Itorralba, Sabine Mai
The advent of super-resolution microscopy allowed for new insights into cellular and physiological processes of normal and diseased cells. In this study, we report for the first time on the super-resolved DNA structure of buccal cells from patients with Alzheimer's disease (AD) versus age- and gender-matched healthy, non-caregiver controls. In this super-resolution study cohort of 74 participants, buccal cells were collected and their spatial DNA organization in the nucleus examined by 3D Structured Illumination Microscopy (3D-SIM)...
December 20, 2016: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/27929156/correlation-of-annealing-time-with-crystal-structure-composition-and-electronic-properties-of-ch3nh3pbi3-xclx-mixed-halide-perovskite-films
#20
Maryline Ralaiarisoa, Yan Busby, Johannes Frisch, Ingo Salzmann, Jean-Jacques Pireaux, Norbert Koch
Using 3D imaging with time-of-flight secondary ion mass spectrometry (ToF-SIMS) complemented by grazing-incidence X-ray diffraction (GIXRD), we spatially resolve changes in both the composition and structure of CH3NH3I3-xClx perovskite films on conducting polymer substrates at different annealing stages, in particular, before and after complete perovskite crystallization. The early stage of annealing is characterized by phase separation throughout the entire film into domains with perovskite and domains with a dominating chloride-rich phase...
December 21, 2016: Physical Chemistry Chemical Physics: PCCP
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